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Comprehensive analysis of DNA methylation data with RnBeads.

Assenov Y, Müller F, Lutsik P, Walter J, Lengauer T, Bock C - Nat. Methods (2014)

Bottom Line: RnBeads is a software tool for large-scale analysis and interpretation of DNA methylation data, providing a user-friendly analysis workflow that yields detailed hypertext reports (http://rnbeads.mpi-inf.mpg.de/).Supported assays include whole-genome bisulfite sequencing, reduced representation bisulfite sequencing, Infinium microarrays and any other protocol that produces high-resolution DNA methylation data.Notable applications of RnBeads include the analysis of epigenome-wide association studies and epigenetic biomarker discovery in cancer cohorts.

View Article: PubMed Central - PubMed

Affiliation: Max Planck Institute for Informatics, Saarbrücken, Germany.

ABSTRACT
RnBeads is a software tool for large-scale analysis and interpretation of DNA methylation data, providing a user-friendly analysis workflow that yields detailed hypertext reports (http://rnbeads.mpi-inf.mpg.de/). Supported assays include whole-genome bisulfite sequencing, reduced representation bisulfite sequencing, Infinium microarrays and any other protocol that produces high-resolution DNA methylation data. Notable applications of RnBeads include the analysis of epigenome-wide association studies and epigenetic biomarker discovery in cancer cohorts.

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Related in: MedlinePlus

RnBeads workflow for analyzing large-scale DNA methylation dataThe RnBeads workflow consists of seven modules and is essentially self-configuring based on a sample annotation table provided by the user. Each module generates part of the RnBeads hypertext report, which includes method descriptions, diagrams, and links to data tables. Furthermore, all data and annotations are stored in RnBSet objects to facilitate custom analysis workflows in R, and they are exported for visualization using genome browsers and follow-up analyses using other software tools.IDAT, signal intensity data; GS, Illumina GenomeStudio data; TAB, TAB-delimited data; GEO, Gene Expression Omnibus data.
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Figure 1: RnBeads workflow for analyzing large-scale DNA methylation dataThe RnBeads workflow consists of seven modules and is essentially self-configuring based on a sample annotation table provided by the user. Each module generates part of the RnBeads hypertext report, which includes method descriptions, diagrams, and links to data tables. Furthermore, all data and annotations are stored in RnBSet objects to facilitate custom analysis workflows in R, and they are exported for visualization using genome browsers and follow-up analyses using other software tools.IDAT, signal intensity data; GS, Illumina GenomeStudio data; TAB, TAB-delimited data; GEO, Gene Expression Omnibus data.

Mentions: To be able to support all protocols for large-scale DNA methylation mapping, RnBeads builds upon existing software tools that can convert raw data into high-resolution DNA methylation profiles. Sequencing data should be preprocessed prior to running RnBeads using software tools such as Bismark9, BSMAP10 and/or Bis-SNP11 (for WGBS/RRBS), MEDIPS12, MEDUSA13 or BayMeth14 (for MeDIP-seq), or methylCRF6 (for MRE-seq). Raw IDAT files from Infinium 450k experiments can be imported directly into RnBeads, in which case the preprocessing and normalization are performed by RnBeads using low-level functionality imported from other R/Bioconductor packages (methylumi, minfi and wateRmelon, cf. Supplementary Table 1). Performing Infinium data normalization in directly RnBeads has practical advantages (e.g., it allows RnBeads to use Infinium quality control probes for pinpointing problematic samples), but it is also possible to load already normalized Infinium data into RnBeads, for example when importing data from the Gene Expression Omnibus resource or from the Illumina GenomeStudio software. In addition to data import, the core workflow of RnBeads comprises quality control, preprocessing and filtering, generation of genome browser tracks and data tables, optional inference of confounding covariates (e.g., different cell type compositions), exploratory analysis and differential DNA methylation analysis (Figure 1 and Online Methods).


Comprehensive analysis of DNA methylation data with RnBeads.

Assenov Y, Müller F, Lutsik P, Walter J, Lengauer T, Bock C - Nat. Methods (2014)

RnBeads workflow for analyzing large-scale DNA methylation dataThe RnBeads workflow consists of seven modules and is essentially self-configuring based on a sample annotation table provided by the user. Each module generates part of the RnBeads hypertext report, which includes method descriptions, diagrams, and links to data tables. Furthermore, all data and annotations are stored in RnBSet objects to facilitate custom analysis workflows in R, and they are exported for visualization using genome browsers and follow-up analyses using other software tools.IDAT, signal intensity data; GS, Illumina GenomeStudio data; TAB, TAB-delimited data; GEO, Gene Expression Omnibus data.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4216143&req=5

Figure 1: RnBeads workflow for analyzing large-scale DNA methylation dataThe RnBeads workflow consists of seven modules and is essentially self-configuring based on a sample annotation table provided by the user. Each module generates part of the RnBeads hypertext report, which includes method descriptions, diagrams, and links to data tables. Furthermore, all data and annotations are stored in RnBSet objects to facilitate custom analysis workflows in R, and they are exported for visualization using genome browsers and follow-up analyses using other software tools.IDAT, signal intensity data; GS, Illumina GenomeStudio data; TAB, TAB-delimited data; GEO, Gene Expression Omnibus data.
Mentions: To be able to support all protocols for large-scale DNA methylation mapping, RnBeads builds upon existing software tools that can convert raw data into high-resolution DNA methylation profiles. Sequencing data should be preprocessed prior to running RnBeads using software tools such as Bismark9, BSMAP10 and/or Bis-SNP11 (for WGBS/RRBS), MEDIPS12, MEDUSA13 or BayMeth14 (for MeDIP-seq), or methylCRF6 (for MRE-seq). Raw IDAT files from Infinium 450k experiments can be imported directly into RnBeads, in which case the preprocessing and normalization are performed by RnBeads using low-level functionality imported from other R/Bioconductor packages (methylumi, minfi and wateRmelon, cf. Supplementary Table 1). Performing Infinium data normalization in directly RnBeads has practical advantages (e.g., it allows RnBeads to use Infinium quality control probes for pinpointing problematic samples), but it is also possible to load already normalized Infinium data into RnBeads, for example when importing data from the Gene Expression Omnibus resource or from the Illumina GenomeStudio software. In addition to data import, the core workflow of RnBeads comprises quality control, preprocessing and filtering, generation of genome browser tracks and data tables, optional inference of confounding covariates (e.g., different cell type compositions), exploratory analysis and differential DNA methylation analysis (Figure 1 and Online Methods).

Bottom Line: RnBeads is a software tool for large-scale analysis and interpretation of DNA methylation data, providing a user-friendly analysis workflow that yields detailed hypertext reports (http://rnbeads.mpi-inf.mpg.de/).Supported assays include whole-genome bisulfite sequencing, reduced representation bisulfite sequencing, Infinium microarrays and any other protocol that produces high-resolution DNA methylation data.Notable applications of RnBeads include the analysis of epigenome-wide association studies and epigenetic biomarker discovery in cancer cohorts.

View Article: PubMed Central - PubMed

Affiliation: Max Planck Institute for Informatics, Saarbrücken, Germany.

ABSTRACT
RnBeads is a software tool for large-scale analysis and interpretation of DNA methylation data, providing a user-friendly analysis workflow that yields detailed hypertext reports (http://rnbeads.mpi-inf.mpg.de/). Supported assays include whole-genome bisulfite sequencing, reduced representation bisulfite sequencing, Infinium microarrays and any other protocol that produces high-resolution DNA methylation data. Notable applications of RnBeads include the analysis of epigenome-wide association studies and epigenetic biomarker discovery in cancer cohorts.

Show MeSH
Related in: MedlinePlus